Hi,

I'm sorry to hear you're having issues. It sounds like you're working with large segmentation images, this slows down the process a lot. If possible, it can help to downsample these (this may not be possible if the objects you're trying to quantify are very small). You can also turn off coordinate extraction in Nutil, this should improve the processing speed. I would also try running with 23 cores (1 less than the max). If you still have issues, feel free to send me an example dataset (1 segmentation and corresponding atlas map, json file containing the registration info and your .nut file from Nutil). I can then investigate further. Email support@ebrains.eu, that the issue is related to brain atlases and should be directed to Sharon Yates. 

Best regards,

Sharon

Originally posted by cicechen:

Thank you for your help! I was able to download it, but when I tried running nutil on a large batch (144 images), I encountered the problem that nutil reports images were not found. I'm certain that images are all in the folders and I suspect it's a computational power issue. However, I'm using a computer with 24 cores and decreased the amount of threads to less than 10. I either still have the same issue or Nutil just started running really slow (it run 1% in 8 hrs) after reaching around 30%. I was wondering if you could help me with that please. Thank you!

 

Wed Mar 5 15:44:22 2025 : Error opening file: C:/Users/CNDRUSER/Desktop/QVN/Input/CC17_1_2413_44_55_s048.png

Wed Mar 5 15:44:22 2025 : Error opening file (size 0): C/Users/CNDRUSER/Desktop/QVN/Input/CC17_1_2413_44_55_5048.png